setwd('/projects/pytrik/sc_adipose/analyze_10x_fluidigm/notebooks/')
.libPaths('/home/cbmr/pytrik/libraries/')
setwd('/projects/pytrik/sc_adipose/analyze_10x_fluidigm/')
library(Seurat)
## Loading required package: ggplot2
## Loading required package: cowplot
## 
## Attaching package: 'cowplot'
## The following object is masked from 'package:ggplot2':
## 
##     ggsave
## Loading required package: Matrix

For the alignment 30 subspaces were aligned. Below datasets are loaded with different runs of tSNE (on the first 10, 20 and 30 aligned CC’s).

aligned.10 <- readRDS('../data/10x_cca30-aligned_tsne-1-10.rds')
aligned.20 <- readRDS('../data/10x_cca30-aligned_tsne-1-20.rds')
aligned.30 <- readRDS('../data/10x_cca30-aligned_tsne-1-30.rds')

aligned.cc.10 <- readRDS('../data/10x_ccregout_cca30-aligned_tsne-1-10.rds')
aligned.cc.20 <- readRDS('../data/10x_ccregout_cca30-aligned_tsne-1-20.rds')
aligned.cc.30 <- readRDS('../data/10x_ccregout_cca30-aligned_tsne-1-30.rds')

TSNEPlots

TSNEPlot(aligned.10, group.by='sample_name', pt.size=0.1)

TSNEPlot(aligned.10, group.by='Phase', pt.size=0.1)

TSNEPlot(aligned.20, group.by='sample_name', pt.size=0.1)

TSNEPlot(aligned.20, group.by='Phase', pt.size=0.1)

TSNEPlot(aligned.30, group.by='sample_name', pt.size=0.1)

TSNEPlot(aligned.30, group.by='Phase', pt.size=0.1)

TSNEPlots of alignment on CC regressed out data.

TSNEPlot(aligned.cc.10, group.by='sample_name', pt.size=0.1)

TSNEPlot(aligned.cc.10, group.by='Phase', pt.size=0.1)

TSNEPlot(aligned.cc.10, group.by='sample_name2', pt.size=0.1)

TSNEPlot(aligned.cc.20, group.by='sample_name', pt.size=0.1)

TSNEPlot(aligned.cc.20, group.by='sample_name2', pt.size=0.1)

TSNEPlot(aligned.cc.20, group.by='Phase', pt.size=0.1)

TSNEPlot(aligned.cc.30, group.by='sample_name', pt.size=0.1)

TSNEPlot(aligned.cc.30, group.by='sample_name2', pt.size=0.1)